miRNA: 3'- uCUGCGGGGUGCgAagaCUGCu--GUug -5'
miRNA: 3'- -UCugCGGGGUgcgaagaCUGCUGUUG- -5'
miRNA: 3'- -UCUGCGGGgUGCGAagAC-----UGCUGUUg -5'
miRNA: 3'- -UCUGcgGGGUGCGa-----AGACUGCUGUUG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 22107 | 5' | -55 | NC_004927.1 | + | 10384 | 0.66 | 0.808045 |
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Target: 5'- cGACGCCCCACGgUgg-GGCGuuuCGc- -3' miRNA: 3'- uCUGCGGGGUGCgAagaCUGCu--GUug -5' |
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| 22107 | 5' | -55 | NC_004927.1 | + | 70632 | 0.66 | 0.798639 |
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Target: 5'- uGGugGCCCCGac-----GACGACGACg -3' miRNA: 3'- -UCugCGGGGUgcgaagaCUGCUGUUG- -5' |
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| 22107 | 5' | -55 | NC_004927.1 | + | 65606 | 0.66 | 0.798639 |
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Target: 5'- gGGGCGCUCgACGCUggUGuuccaGCGGCGAa -3' miRNA: 3'- -UCUGCGGGgUGCGAagAC-----UGCUGUUg -5' |
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| 22107 | 5' | -55 | NC_004927.1 | + | 46917 | 0.72 | 0.455113 |
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Target: 5'- aGGACaaCCCGCGUgacgccUUUGACGACGGCg -3' miRNA: 3'- -UCUGcgGGGUGCGa-----AGACUGCUGUUG- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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